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Nature. 2017 Dec 21;552(7685):415-420. doi: 10.1038/nature25157. Epub 2017 Dec 13.

Evolution of a designed protein assembly encapsulating its own RNA genome.

Author information

1
Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
2
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
3
Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, USA.
4
Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA.
5
Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, USA.
6
Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA.
7
Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, Washington 98195, USA.
8
College of Arts & Sciences, University of Washington, Seattle, Washington 98195, USA.
9
School of Public Health, University of Washington, Seattle, Washington 98195, USA.
10
Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.

Abstract

The challenges of evolution in a complex biochemical environment, coupling genotype to phenotype and protecting the genetic material, are solved elegantly in biological systems by the encapsulation of nucleic acids. In the simplest examples, viruses use capsids to surround their genomes. Although these naturally occurring systems have been modified to change their tropism and to display proteins or peptides, billions of years of evolution have favoured efficiency at the expense of modularity, making viral capsids difficult to engineer. Synthetic systems composed of non-viral proteins could provide a 'blank slate' to evolve desired properties for drug delivery and other biomedical applications, while avoiding the safety risks and engineering challenges associated with viruses. Here we create synthetic nucleocapsids, which are computationally designed icosahedral protein assemblies with positively charged inner surfaces that can package their own full-length mRNA genomes. We explore the ability of these nucleocapsids to evolve virus-like properties by generating diversified populations using Escherichia coli as an expression host. Several generations of evolution resulted in markedly improved genome packaging (more than 133-fold), stability in blood (from less than 3.7% to 71% of packaged RNA protected after 6 hours of treatment), and in vivo circulation time (from less than 5 minutes to approximately 4.5 hours). The resulting synthetic nucleocapsids package one full-length RNA genome for every 11 icosahedral assemblies, similar to the best recombinant adeno-associated virus vectors. Our results show that there are simple evolutionary paths through which protein assemblies can acquire virus-like genome packaging and protection. Considerable effort has been directed at 'top-down' modification of viruses to be safe and effective for drug delivery and vaccine applications; the ability to design synthetic nanomaterials computationally and to optimize them through evolution now enables a complementary 'bottom-up' approach with considerable advantages in programmability and control.

PMID:
29236688
PMCID:
PMC5927965
DOI:
10.1038/nature25157
[Indexed for MEDLINE]
Free PMC Article

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